md summary and log shall follow same naming scheme as the rest of the files

[alinelena]

No description provided.

[ElliottKasoar]

The inconvenient thing for this is that the naming schemes depend on how we instantiate the MD classes.

This isn't too much of a problem for the summary, since we only create it just before dyn.run, but the log is currently created via SinglePoint so that the logs are all shared, and I'm not sure there's a particularly tidy way around that.

This would also mean we can't have the defaults in the CLI help, but that's probably fine.